HYPDA_CLODI
ID HYPDA_CLODI Reviewed; 302 AA.
AC A0A069AMK2;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2014, sequence version 1.
DT 03-AUG-2022, entry version 51.
DE RecName: Full=Trans-4-hydroxy-L-proline dehydratase activating enzyme {ECO:0000303|PubMed:28183913};
DE EC=1.97.1.- {ECO:0000305|PubMed:28183913};
DE AltName: Full=Glycyl-radical enzyme activating enzyme PflE {ECO:0000305|PubMed:28183913};
DE Short=GRE activating enzyme {ECO:0000305|PubMed:28183913};
GN Name=pflE {ECO:0000303|Ref.1}; Synonyms=csdA {ECO:0000312|EMBL:SJP87434.1};
GN ORFNames=BGU81_07855 {ECO:0000312|EMBL:PBG28509.1},
GN BN1095_640055 {ECO:0000312|EMBL:CDT69048.1},
GN BN1096_740113 {ECO:0000312|EMBL:CDS89457.1},
GN BN1097_360076 {ECO:0000312|EMBL:CDS85121.1},
GN C7R55_12960 {ECO:0000312|EMBL:PSJ82865.1},
GN DDG63_17935 {ECO:0000312|EMBL:AWH82816.1},
GN SAMEA3374989_01496 {ECO:0000312|EMBL:SJP87434.1};
OS Clostridioides difficile (Peptoclostridium difficile).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptostreptococcaceae;
OC Clostridioides.
OX NCBI_TaxID=1496 {ECO:0000312|EMBL:CDS89457.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=7032989 {ECO:0000312|EMBL:CDT69048.1}, and
RC 7032994 {ECO:0000312|EMBL:CDS85121.1};
RA Monot M.;
RL Submitted (JUL-2014) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=6636-R/ST48 {ECO:0000312|EMBL:PBG28509.1};
RA Kociolek L.K., Ozer E.A.;
RT "Genomic characterization of C. difficile isolates from children.";
RL Submitted (NOV-2016) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VRECD0007 {ECO:0000312|EMBL:SJP87434.1};
RG Pathogen Informatics;
RL Submitted (FEB-2017) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HS-FS_0042_01 {ECO:0000312|EMBL:PSJ82865.1};
RA Stone N., Sahl J., Wagner D.;
RT "Clinical sequencing of C. difficile.";
RL Submitted (MAR-2018) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CD161 {ECO:0000312|EMBL:AWH82816.1};
RA Su H.;
RL Submitted (APR-2018) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION.
RC STRAIN=70-100-2010;
RX PubMed=28183913; DOI=10.1126/science.aai8386;
RA Levin B.J., Huang Y.Y., Peck S.C., Wei Y., Martinez-Del Campo A.,
RA Marks J.A., Franzosa E.A., Huttenhower C., Balskus E.P.;
RT "A prominent glycyl radical enzyme in human gut microbiomes metabolizes
RT trans-4-hydroxy-L-proline.";
RL Science 355:1-28(2017).
CC -!- FUNCTION: Catalyzes activation of the trans-4-hydroxy-L-proline
CC dehydratase under anaerobic conditions by generation of an organic free
CC radical on a glycine residue, via a homolytic cleavage of S-adenosyl-L-
CC methionine (SAM). Is involved in the anaerobic degradation of 4-
CC hydroxyproline. {ECO:0000269|PubMed:28183913}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycyl-[protein] + reduced [flavodoxin] + S-adenosyl-L-
CC methionine = 5'-deoxyadenosine + glycin-2-yl radical-[protein] + H(+)
CC + L-methionine + semiquinone [flavodoxin]; Xref=Rhea:RHEA:61976,
CC Rhea:RHEA-COMP:10622, Rhea:RHEA-COMP:14480, Rhea:RHEA-COMP:15993,
CC Rhea:RHEA-COMP:15994, ChEBI:CHEBI:15378, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:29947, ChEBI:CHEBI:32722, ChEBI:CHEBI:57618,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:140311;
CC Evidence={ECO:0000305|PubMed:28183913};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:Q30W71};
CC Note=Binds 2 [4Fe-4S] cluster. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000250|UniProtKB:Q30W71};
CC -!- SIMILARITY: Belongs to the organic radical-activating enzymes family.
CC {ECO:0000305}.
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DR EMBL; LK932372; CDS85121.1; -; Genomic_DNA.
DR EMBL; LK932529; CDS89457.1; -; Genomic_DNA.
DR EMBL; LK933338; CDT69048.1; -; Genomic_DNA.
DR EMBL; MPEQ01000010; PBG28509.1; -; Genomic_DNA.
DR EMBL; FUNQ01000002; SJP87434.1; -; Genomic_DNA.
DR EMBL; PXZF01000010; PSJ82865.1; -; Genomic_DNA.
DR EMBL; CP029154; AWH82816.1; -; Genomic_DNA.
DR RefSeq; WP_003432388.1; NZ_WBMC01000016.1.
DR AlphaFoldDB; A0A069AMK2; -.
DR SMR; A0A069AMK2; -.
DR EnsemblBacteria; PBG28509; PBG28509; BGU81_07855.
DR EnsemblBacteria; SJP87434; SJP87434; SAMEA3374989_01496.
DR GeneID; 66355777; -.
DR PATRIC; fig|1496.1371.peg.375; -.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; ISS:UniProtKB.
DR GO; GO:0043364; F:glycyl-radical enzyme activating activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR017896; 4Fe4S_Fe-S-bd.
DR InterPro; IPR017900; 4Fe4S_Fe_S_CS.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR040074; BssD/PflA/YjjW.
DR InterPro; IPR034457; Organic_radical-activating.
DR InterPro; IPR012839; Organic_radical_activase.
DR InterPro; IPR001989; Radical_activat_CS.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR30352; PTHR30352; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF000371; PFL_act_enz; 1.
DR SFLD; SFLDG01118; activating_enzymes__group_2; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR PROSITE; PS00198; 4FE4S_FER_1; 1.
DR PROSITE; PS51379; 4FE4S_FER_2; 2.
DR PROSITE; PS01087; RADICAL_ACTIVATING; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Oxidoreductase; Repeat;
KW S-adenosyl-L-methionine.
FT CHAIN 1..302
FT /note="Trans-4-hydroxy-L-proline dehydratase activating
FT enzyme"
FT /id="PRO_0000445029"
FT DOMAIN 14..297
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 45..74
FT /note="4Fe-4S ferredoxin-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT DOMAIN 75..103
FT /note="4Fe-4S ferredoxin-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 28
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4"
FT BINDING 32
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4"
FT BINDING 34..36
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4"
FT BINDING 35
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4"
FT BINDING 54
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q30W71"
FT BINDING 57
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q30W71"
FT BINDING 60
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q30W71"
FT BINDING 93
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q30W71"
FT BINDING 133
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4"
FT BINDING 183..185
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4"
FT BINDING 257
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4"
SQ SEQUENCE 302 AA; 34376 MW; E8433F289198C84B CRC64;
MNPLVINLQK CSIHDGPGIR STVFFKGCPL ECVWCHNPES QTYTKQVLYN EERCSKCEAC
INICPHKAIY KGETKICLDQ DKCEFCETCL DYCVNNAREI VGQEYSVRDL VKEIEKDRIF
YEESGGGVTL SGGEVMAQDM DFICGVINMC KSKGIHVAID TCGYAKSENY ERVAKCADLF
LYDIKLIDED KHIKFTGKSN DLILKNVKIL SELGANINIR IPLIVGVNVD DENLEVKKMI
EFLKPLNIQA VSLLPYHNIG KHKYDKIYKK YEGEELQRPS EEKLEEIKRL FEASNFNTKI
GG
